Structural studies of RNase P

Summary

Principal Investigator: ALFONSO MONDRAGON
Abstract: DESCRIPTION (provided by applicant): Ribonuclease P (RNase P) is a ribonucleoprotein complex responsible for processing many different RNA molecules in the cell. It is found in almost all organisms, from bacteria to humans, and is composed of one essential RNA subunit and one or more protein subunits. The RNA component is responsible for catalysis as it can process RNA in vitro in the absence of protein. The only common RNase P function in all organisms is the 5'end maturation of transfer RNA (tRNA). RNase P was one of the first catalytic RNA molecules discovered and its study has been pivotal to our understanding of the role of RNA molecules in catalysis. RNase P is a true multi-turnover ribozyme that recognizes its substrate in trans and one of only two universal ribozymes. The knowledge of the structure and function of RNase P promises to provide important and relevant information on a key ribozyme involved in a central cellular process common to all organisms and also to further our understanding of the structure and function of large RNA molecules. This proposal is concerned with the structure and function of RNase P. In the past few years we have made substantial progress in our studies, including solving the structure of the complex formed by Thermotoga maritima RNase P holoenzyme and mature tRNA. The structural studies of the holoenzyme/tRNA complex show that all RNase P ribozymes share a common, RNA-based mechanism of RNA cleavage and recognition where the protein component increases RNase P functionality by accurately positioning the 5'leader pre-tRNA substrate and by contacting conserved regions of the P RNA structure. The structure also shows that RNase P utilizes shape complementarity, specific RNA-RNA contacts, and intermolecular base pairing to recognize its substrate efficiently and that both P RNA and the pre-tRNA help to coordinate two catalytically important metal ions essential for the mechanism of pre-tRNA cleavage. For the next period we propose to continue and expand our structural studies of RNase P. The specific aims for this proposal are: 1) to determine the three dimensional structure of complexes of RNase P holoenzyme with different substrates, 2) to determine the structure of complexes of RNase P holoenzyme with pre-tRNA and transition state analogues and, 3) to study the role of the universally conserved regions in the structure of RNase P and also the role of important amino acids involved in leader recognition. The work is based on a combination of molecular biology and biochemical methods to produce and characterize the molecules that we require for our work and X-ray crystallography to solve their atomic structures. The work on RNase P has important implications for health related studies. RNase P is a promising target for the development of new chemotherapeutics as the specificity of RNase P can be altered to create molecules that degrade target RNA molecules.
Funding Period: 1999-09-01 - 2016-02-29
more information: NIH RePORT

Top Publications

  1. ncbi Structure of ribonuclease P--a universal ribozyme
    Alfredo Torres-Larios
    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208, USA
    Curr Opin Struct Biol 16:327-35. 2006
  2. pmc Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA
    Nicholas J Reiter
    Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
    Nature 468:784-9. 2010
  3. pmc Emerging structural themes in large RNA molecules
    Nicholas J Reiter
    Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
    Curr Opin Struct Biol 21:319-26. 2011
  4. pmc The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning
    Nicholas J Reiter
    Department of Molecular Biosciences, Northwestern University, 2205 Tech Dr, Evanston, IL 60208, USA
    Nucleic Acids Res 40:10384-93. 2012
  5. ncbi Structural studies of RNase P
    ALFONSO MONDRAGON
    Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
    Annu Rev Biophys 42:537-57. 2013
  6. pmc Structure and function of the T-loop structural motif in noncoding RNAs
    Clarence W Chan
    Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
    Wiley Interdiscip Rev RNA 4:507-22. 2013

Research Grants

  1. Molecular Mechanisms of Signal Transduction by Two-Component Regulatory Systems
    Robert B Bourret; Fiscal Year: 2013
  2. Studies of Isoprenoid Biosynthesis
    CHARLES DALE POULTER; Fiscal Year: 2013
  3. Structural bases of the functions of RNA-protein machines
    THOMAS ARTHUR STEITZ; Fiscal Year: 2013
  4. Structure and Mechanism in DNA Excision Repair
    GREGORY LAWRENCE VERDINE; Fiscal Year: 2013
  5. Coupling of structure and dynamics in RNA catalysis
    BARBARA LYNN GOLDEN; Fiscal Year: 2013
  6. Resolution Mechanisms in Acute Inflammation: Resolution Pharmacology
    CHARLES NICHOLAS SERHAN; Fiscal Year: 2013
  7. Structure and function of RNase P
    Michael E Harris; Fiscal Year: 2013
  8. Enzymology of RNA Processing
    Carol A Fierke; Fiscal Year: 2013
  9. Structural regulation of ribozyme catalysis
    William G Scott; Fiscal Year: 2013
  10. RNA CONFORMATION AND CATALYSIS
    David P Bartel; Fiscal Year: 2013

Detail Information

Publications7

  1. ncbi Structure of ribonuclease P--a universal ribozyme
    Alfredo Torres-Larios
    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208, USA
    Curr Opin Struct Biol 16:327-35. 2006
    ..Comparison of these structures reveals a highly conserved core that comprises two universally conserved structural modules. Interestingly, the same structural core can be found in the context of different scaffolds...
  2. pmc Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA
    Nicholas J Reiter
    Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
    Nature 468:784-9. 2010
    ..The active site structure and conserved RNase P-tRNA contacts suggest a universal mechanism of catalysis by RNase P...
  3. pmc Emerging structural themes in large RNA molecules
    Nicholas J Reiter
    Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
    Curr Opin Struct Biol 21:319-26. 2011
    ..These findings broaden our understanding of RNA folding and tertiary structure stabilization, illustrating how large, complex RNAs assemble into unique structures to perform recognition and catalysis...
  4. pmc The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning
    Nicholas J Reiter
    Department of Molecular Biosciences, Northwestern University, 2205 Tech Dr, Evanston, IL 60208, USA
    Nucleic Acids Res 40:10384-93. 2012
    ..This suggests a synergistic coupling between transition state formation and substrate positioning via interactions with the leader...
  5. ncbi Structural studies of RNase P
    ALFONSO MONDRAGON
    Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
    Annu Rev Biophys 42:537-57. 2013
    ....
  6. pmc Structure and function of the T-loop structural motif in noncoding RNAs
    Clarence W Chan
    Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
    Wiley Interdiscip Rev RNA 4:507-22. 2013
    ..Additionally, the potential application for T-loops as interaction modules is also discussed...

Research Grants30

  1. Molecular Mechanisms of Signal Transduction by Two-Component Regulatory Systems
    Robert B Bourret; Fiscal Year: 2013
    ..Fundamental principles of signal transduction may also emerge. ..
  2. Studies of Isoprenoid Biosynthesis
    CHARLES DALE POULTER; Fiscal Year: 2013
    ....
  3. Structural bases of the functions of RNA-protein machines
    THOMAS ARTHUR STEITZ; Fiscal Year: 2013
    ..Also of interest will be the ways in which the structures and properties of RNA molecules can be utilized to carry out various biological functions often analogous to those performed by proteins. ..
  4. Structure and Mechanism in DNA Excision Repair
    GREGORY LAWRENCE VERDINE; Fiscal Year: 2013
    ..Together, these studies aim to provide a comprehensive molecular-level framework for understanding two very important but very different strategies for seeking out and destroying genotoxic lesions in DNA. ..
  5. Coupling of structure and dynamics in RNA catalysis
    BARBARA LYNN GOLDEN; Fiscal Year: 2013
    ..We anticipate that the results of this study will provide clues as to the catalytic strategies of many ribozymes, some of which will be therapeutic targets. ..
  6. Resolution Mechanisms in Acute Inflammation: Resolution Pharmacology
    CHARLES NICHOLAS SERHAN; Fiscal Year: 2013
    ..Selected synthetic SPM will be scaled-up for demonstration of their unique mode of action in vivo in a resolution pharmacology core using experimental disease models. Our broad goal is to bring forth new treatments in resolution. ..
  7. Structure and function of RNase P
    Michael E Harris; Fiscal Year: 2013
    ..Additionally we are developing methods to detect ion binding at individual phosphates using isotope-edited Raman. ..
  8. Enzymology of RNA Processing
    Carol A Fierke; Fiscal Year: 2013
    ....
  9. Structural regulation of ribozyme catalysis
    William G Scott; Fiscal Year: 2013
    ....
  10. RNA CONFORMATION AND CATALYSIS
    David P Bartel; Fiscal Year: 2013
    ....
  11. Mechanisms Underlying Chronic Lung Pathology
    Wayne Mitzner; Fiscal Year: 2013
    ..This tightly integrated, synergistic program will thereby provide new insights into the mechanisms that underlie the pathogenic progression of chronic lung diseases. ..
  12. Mechanisms of Radical-Dependent Biological Methylation
    Squire J Booker; Fiscal Year: 2013
    ..We will characterize this reaction further using a variety of kinetic, spectroscopic, and biochemical techniques, and provide biochemical and/or structural evidence for each of the postulated intermediates in the reaction. ..
  13. Mapping Allosteric Cooperativity in Protein Kinases
    Gianluigi Veglia; Fiscal Year: 2013
    ..Understanding how allosteric signals propagate and trigger binding cooperativity will help in designing new strategies to control (by inhibiting or tuning) kinase activity for innovative therapies to treat disease. ..
  14. Structural Studies of Telomerase Holoenzyme
    EDWARD JOHN MIRACCO; Fiscal Year: 2013
    ..These experiments will reveal the complete structure of a telomerase holoenzyme as well as offer insight into what roles intermolecular contacts and subunit movement play in telomere catalysis. ..
  15. Dynamic Properties that Enhance Enzyme Function
    Sidney M Hecht; Fiscal Year: 2013
    ..The enzyme DHFR, which is the target of important antineoplastic and antimicrobial drugs, will be the focus of our efforts. ..